This study compared the presence of 6 periodontopathic bacteria in whole saliva and subgingival plaque of 202 subjects. The test bacteria were identified using a 16S rRNA-based PCR detection method. Each study subject contributed a whole saliva sample and a paper point sample pooled from the deepest periodontal pocket in each quadrant of the dentition. The kappa test revealed a fair agreement between the presence of Porphyromonas gingivalis, Prevotella intermedia, and Treponema denticola in whole saliva and periodontal pocket samples (kappa > 0.4). The McNemar test showed that the differences between sample types were due to a more frequent detection of the 3 organisms in whole saliva than in periodontal pocket samples (P < 0.01). Prevotella nigrescens also was detected more frequently in whole saliva than in periodontal pocket samples (P < 0.01; McNemar test). Although little agreement between samples was found for Actinobacillus actinomycetemcomitans and Bacteroides forsythus (kappa < or = 0.4), neither whole saliva nor pocket samples showed better detection for these 2 species (P < 0.01, McNemar test). The results indicate that whole saliva is superior to pooled periodontal pocket samples to detect P. gingivalis, P. intermedia, P. nigrescens, and T. denticola in the oral cavity. The detection of oral A. actinomycetemcomitans and B. forsythus with reasonably good accuracy may require both whole saliva and periodontal pocket samples.